peptidew:lib:humanhcd20160503

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peptidew:lib:humanhcd20160503 [2018/08/07 09:44]
peptidew:lib:humanhcd20160503 [2020/02/25 15:06] (current)
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 +====== Human HCD Library ======
 +=====  Peptide Library (September 23, 2016) =====
 +
 +The human HCD library was created from data available on public repositories:​
 +
 +  * ProteomeXchange - [[http://​www.proteomexchange.org/​|http://​www.proteomexchange.org]]
 +
 +{{page>​newfiles_warning}}
 +
 +<WRAP center group 80%>
 +^ File - Description ^ Size ^ Link ^
 +| **human_hcd_selected.msp.tar.gz** \\ Library of selected spectra in plain ASCII text (msp format). This format can be used as an exchange format. It is also directly readable by some software applications,​ like Skyline, after unzipping. |  2.2GB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2016_09_23/​human_hcd_selected.msp.tar.gz|Download]] |
 +| **human_hcd_selected_part1.tar.gz** \\ **human_hcd_selected_part2.tar.gz** \\ \\ Library of selected spectra in NIST binary format (two parts). The folders generated by extracting these packages can be used directly by [[peptidew:​mspepsearch|MS Search or MSPepSearch]] and by the MSPepSearch node within Proteome Discoverer. |  5.1GB \\ 379MB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2016_09_23/​human_hcd_selected_part1.tar.gz|Download1]] \\ [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2016_09_23/​human_hcd_selected_part2.tar.gz|Download2]]| ​
 +| **human_fasta.tar.gz** - FASTA file used to create the library.| ​ 15MB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2016_05_03/​human_fasta.tar.gz|Download]] | 
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​2016_09_23/​md5_checklist.chk|Download]] | 
 +</​WRAP>​
 +
 +  * Total number of Spectra: **1,​127,​970**
 +  * Unique Peptide Sequences: **320,824**
 +  * Total Proteins in FASTA file used: **60,384**
 +  * Proteome Coverage: **27.51%**
 +
 +
 +=====  Decoy Library (February 21, 2020) =====
 +
 +The decoy library (sequence reversed) was created based on the methods described in the paper: \\ 
 +**Zhang, Zheng, et al.** //"​Reverse and random decoy methods for false discovery rate estimation in high mass accuracy peptide spectral library searches."//​ Journal of Proteome Research 17.2 (2018): 846-857.
 +
 +
 +<WRAP center group 80%>
 +^ Decoy Libraries - Description ^ Size ^ Link ^
 +| **human_hcd_selected_decoy.msp.tar.gz** - Library of decoy spectra in plain ASCII text (msp format). This format can be used as an exchange format. It is also directly readable by some software applications,​ like Skyline, after unzipping. |  2.3GB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap-HCD/​human_hcd_selected_decoy.msp.tar.gz|Download]] |
 +| **human_hcd_selected_decoy_1.tar.gz** \\ **human_hcd_selected_decoy_2.tar.gz** \\ \\ Library of decoy spectra in NIST binary format (two parts). The folders generated by extracting these packages can be used directly by [[peptidew:​mspepsearch|MS Search or MSPepSearch]] and by the MSPepSearch node within Proteome Discoverer. |  5.0GB \\ 531MB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap-HCD/​human_hcd_selected_decoy_1.tar.gz|Download1]] \\ [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap-HCD/​human_hcd_selected_decoy_2.tar.gz|Download2]]| ​
 +| **md5_checklist.chk** - MD5 hash file. |  1KB| [[ftp://​chemdata.nist.gov/​download/​peptide_library/​libraries/​human/​HCD/​decoy/​Orbitrap-HCD/​md5_checklist.chk|Download]] |
 +</​WRAP>​
 +
 +{{page>​pepcopyright}}
 +
 +